3.3.2. Variance in Allelic Frequency Due to Change in Chromosomal Somy/Ploidy

In most of the cases, drug resistance in pathogenic microorganism correlates with gene expression changes, which somehow are concordant with the chromosomal ploidy changes. Normalized read depth data are generally used to assess copy number variation as somy estimation does not always show a result in integral values, since it depicts the average of a population of the cell that does not strictly show identical karyotypes. To determine somy, the two-loop method was used [38,63]. Chromosomal somy data analysis of K133WT and K133AS-R shows that most of the chromosomes were disomic. Deflection from this pattern was detected in chromosome number 14 and 32, which were monosomic, while chromosome 5, 8, 20, 23, and 31 displayed the trisomy condition in both K133WT and K133AS-R. Chromosome 12 only was found in the trisomy condition, a unique observation in K133AS-R (Figure 3).

**Figure 3.** Chromosomy estimation in *L. donovani* parental line (K133WT) and artemisinin-resistant lines K133AS-R. The solid line represents median coverage and it was assigned a value of 2, considering that diploid is the principal ploidy state in *Leishmania*. The dotted line represents the calculated values for other somies (blue- monosomy; between two dotted red-trisomy).
